Out of interest, what do you want the waveforms for ? Generating them at 44.1Khz takes quite a lot of the processor time, generating them at 8Khz gives a much lower quality but takes very little processor time.

Looking at the assembly, the ISR is around 30 instructions, so accounting for some over head outside the ISR, generating a sinewave at a 44.1Khz sample rate is using around 2% of the Arduino Due processing time. Its huge improvement over the UNO which would really struggle with 44.1Khz. A lot of the improvement is due to the Due being able to operate on 32 bits at a time, the UNO needs 4 cycles to process 32 bits. Add the faster processor clock and the Due is cruising.